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  <title>GenBank Feature Extractor</title>
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  <div class="category">
    Format Conversion
  </div>

  <div class="program">
    <a href="combine_fasta.html" onmouseover="self.status='Combines multiple FASTA entries into a single sequence.'; return true;" onmouseout="self.status=' '; return true;">-Combine FASTA</a><br />
    <a href="embl_fasta.html" onmouseover="self.status='Returns the entire sequence contained in an EMBL file in FASTA format.'; return true;" onmouseout="self.status=' '; return true;">-EMBL to FASTA</a><br />
    <a href="embl_feat.html" onmouseover="self.status='Parses the feature table of an EMBL file and returns the feature sequences.'; return true;" onmouseout="self.status=' '; return true;">-EMBL Feature Extractor</a><br />
    <a href="embl_trans.html" onmouseover="self.status='Parses the feature table of an EMBL file and returns the protein translations.'; return true;" onmouseout="self.status=' '; return true;">-EMBL Trans Extractor</a><br />
    <a href="filter_dna.html" onmouseover="self.status='Removes non-DNA characters from text.'; return true;" onmouseout="self.status=' '; return true;">-Filter DNA</a><br />
    <a href="filter_protein.html" onmouseover="self.status='Removes non-protein characters from text.'; return true;" onmouseout="self.status=' '; return true;">-Filter Protein</a><br />
    <a href="genbank_fasta.html" onmouseover="self.status='Returns the entire sequence contained in a GenBank file in FASTA format.'; return true;" onmouseout="self.status=' '; return true;">-GenBank to FASTA</a><br />
    <a href="genbank_feat.html" onmouseover="self.status='Parses the feature table of a GenBank file and returns the feature sequences.'; return true;" onmouseout="self.status=' '; return true;">-GenBank Feature Extractor</a><br />
    <a href="genbank_trans.html" onmouseover="self.status='Parses the feature table of a GenBank file and returns the protein translations.'; return true;" onmouseout="self.status=' '; return true;">-GenBank Trans Extractor</a><br />
    <a href="one_to_three.html" onmouseover="self.status='Converts single letter amino acid codes to three letter codes.'; return true;" onmouseout="self.status=' '; return true;">-One to Three</a><br />
    <a href="range_extract_dna.html" onmouseover="self.status='Reads a list of positions and ranges and returns those parts of a DNA sequence.'; return true;" onmouseout="self.status=' '; return true;">-Range Extractor DNA</a><br />
    <a href="range_extract_protein.html" onmouseover="self.status='Reads a list of positions and ranges and returns those parts of a protein sequence.'; return true;" onmouseout="self.status=' '; return true;">-Range Extractor Protein</a><br />
    <a href="rev_comp.html" onmouseover="self.status='Determines the reverse-complement, reverse, or complement of the sequence you enter.'; return true;" onmouseout="self.status=' '; return true;">-Reverse Complement</a><br />
    <a href="split_codons.html" onmouseover="self.status='Separates bases according to codon position.'; return true;" onmouseout="self.status=' '; return true;">-Split Codons</a><br />
    <a href="split_fasta.html" onmouseover="self.status='Converts a FASTA sequence into multiple sequences.'; return true;" onmouseout="self.status=' '; return true;">-Split FASTA</a><br />
    <a href="three_to_one.html" onmouseover="self.status='Converts three letter amino acid codes to one letter codes.'; return true;" onmouseout="self.status=' '; return true;">-Three to One</a><br />
    <a href="window_extract_dna.html" onmouseover="self.status='Returns DNA sequence segments specified by a position and window size.'; return true;" onmouseout="self.status=' '; return true;">-Window Extractor DNA</a><br />
    <a href="window_extract_protein.html" onmouseover="self.status='Returns protein sequence segments specified by a position and window size.'; return true;" onmouseout="self.status=' '; return true;">-Window Extractor Protein</a>
  </div>

  <div class="category">
    Sequence Analysis
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  <div class="program">
    <a href="codon_plot.html" onmouseover="self.status='Plots codon frequency (according to the codon table you enter) for each codon in a DNA sequence.'; return true;" onmouseout="self.status=' '; return true;">-Codon Plot</a><br />
    <a href="codon_usage.html" onmouseover="self.status='Returns a standard codon usage table.'; return true;" onmouseout="self.status=' '; return true;">-Codon Usage</a><br />
    <a href="cpg_islands.html" onmouseover="self.status='Returns a list of potential CpG islands.'; return true;" onmouseout="self.status=' '; return true;">-CpG Islands</a><br />
    <a href="dna_mw.html" onmouseover="self.status='Calculates the molecular weight of DNA sequences.'; return true;" onmouseout="self.status=' '; return true;">-DNA Molecular Weight</a><br />
    <a href="dna_pattern.html" onmouseover="self.status='Returns positions of the patterns you enter.'; return true;" onmouseout="self.status=' '; return true;">-DNA Pattern Find</a><br />
    <a href="dna_stats.html" onmouseover="self.status='Returns basic sequence statistics.'; return true;" onmouseout="self.status=' '; return true;">-DNA Stats</a><br />
    <a href="fuzzy_search_dna.html" onmouseover="self.status='Returns sequences that are identical or similar to a query sequence.'; return true;" onmouseout="self.status=' '; return true;">-Fuzzy Search DNA</a><br />
    <a href="fuzzy_search_protein.html" onmouseover="self.status='Returns sequences that are identical or similar to a query sequence.'; return true;" onmouseout="self.status=' '; return true;">-Fuzzy Search Protein</a><br />
    <a href="ident_sim.html" onmouseover="self.status='Accepts aligned sequences in FASTA format and calculates the identity and similarity of each sequence pair.'; return true;" onmouseout="self.status=' '; return true;">-Ident and Sim</a><br />
    <a href="multi_rev_trans.html" onmouseover="self.status='Can be used to predict a DNA sequence in another species using a protein sequence alignment.'; return true;" onmouseout="self.status=' '; return true;">-Multi Rev Trans</a><br />
    <a href="mutate_for_digest.html" onmouseover="self.status='Finds DNA sequences that can easily be converted to a restriction site.'; return true;" onmouseout="self.status=' '; return true;">-Mutate for Digest</a><br />
    <a href="orf_find.html" onmouseover="self.status='Determines the positions of open reading frames.'; return true;" onmouseout="self.status=' '; return true;">-ORF Finder</a><br />
    <a href="pairwise_align_codons.html" onmouseover="self.status='Returns the optimal global alignment for two coding DNA sequences.'; return true;" onmouseout="self.status=' '; return true;">-Pairwise Align Codons</a><br />
    <a href="pairwise_align_dna.html" onmouseover="self.status='Returns the optimal global alignment for two DNA sequences.'; return true;" onmouseout="self.status=' '; return true;">-Pairwise Align DNA</a><br />
    <a href="pairwise_align_protein.html" onmouseover="self.status='Returns the optimal global alignment for two protein sequences.'; return true;" onmouseout="self.status=' '; return true;">-Pairwise Align Protein</a><br />
    <a href="pcr_primer_stats.html" onmouseover="self.status='Returns a report describing PCR primer properties'; return true;" onmouseout="self.status=' '; return true;">-PCR Primer Stats</a><br />
    <a href="pcr_products.html" onmouseover="self.status='Generates PCR products from a template and two primer sequences.'; return true;" onmouseout="self.status=' '; return true;">-PCR Products</a><br />
    <a href="protein_gravy.html" onmouseover="self.status='Returns the grand average of hydropathy value of protein sequences.'; return true;" onmouseout="self.status=' '; return true;">-Protein GRAVY</a><br />
    <a href="protein_iep.html" onmouseover="self.status='Returns the predicted isoelectric point of protein sequences.'; return true;" onmouseout="self.status=' '; return true;">-Protein Isoelectric Point</a><br />
    <a href="protein_mw.html" onmouseover="self.status='Calculates the molecular weight of protein sequences.'; return true;" onmouseout="self.status=' '; return true;">-Protein Molecular Weight</a><br />
    <a href="protein_pattern.html" onmouseover="self.status='Returns positions of the patterns you enter.'; return true;" onmouseout="self.status=' '; return true;">-Protein Pattern Find</a><br />
    <a href="protein_stats.html" onmouseover="self.status='Returns basic sequence statistics.'; return true;" onmouseout="self.status=' '; return true;">-Protein Stats</a><br />
    <a href="rest_digest.html" onmouseover="self.status='Converts the sequence you enter into restriction fragments.'; return true;" onmouseout="self.status=' '; return true;">-Restriction Digest</a><br />
    <a href="rest_summary.html" onmouseover="self.status='Returns the number and positions of restriction sites.'; return true;" onmouseout="self.status=' '; return true;">-Restriction Summary</a><br />
    <a href="rev_trans.html" onmouseover="self.status='Can be used to convert protein into DNA.'; return true;" onmouseout="self.status=' '; return true;">-Reverse Translate</a><br />
    <a href="translate.html" onmouseover="self.status='Returns the translation in the reading frame you specify.'; return true;" onmouseout="self.status=' '; return true;">-Translate</a>
  </div>

  <div class="category">
    Sequence Figures
  </div>

  <div class="program">
    <a href="color_align_cons.html" onmouseover="self.status='Colors a sequence alignment based on sequence conservation.'; return true;" onmouseout="self.status=' '; return true;">-Color Align Conservation</a><br />
    <a href="color_align_prop.html" onmouseover="self.status='Colors a protein alignment based on biochemical properties of residues.'; return true;" onmouseout="self.status=' '; return true;">-Color Align Properties</a><br />
    <a href="group_dna.html" onmouseover="self.status='Numbers and groups DNA according to your specifications.'; return true;" onmouseout="self.status=' '; return true;">-Group DNA</a><br />
    <a href="group_protein.html" onmouseover="self.status='Numbers and groups amino acids according to your specifications.'; return true;" onmouseout="self.status=' '; return true;">-Group Protein</a><br />
    <a href="primer_map.html" onmouseover="self.status='Shows PCR primer annealing sites, translations, and restriction sites.'; return true;" onmouseout="self.status=' '; return true;">-Primer Map</a><br />
    <a href="rest_map.html" onmouseover="self.status='Shows restriction sites and protein translations.'; return true;" onmouseout="self.status=' '; return true;">-Restriction Map</a><br />
    <a href="trans_map.html" onmouseover="self.status='Shows protein translations.'; return true;" onmouseout="self.status=' '; return true;">-Translation Map</a>
  </div>

  <div class="category">
    Random Sequences
  </div>

  <div class="program">
    <a href="mutate_dna.html" onmouseover="self.status='Introduces random mutations into DNA sequences.'; return true;" onmouseout="self.status=' '; return true;">-Mutate DNA</a><br />
    <a href="mutate_protein.html" onmouseover="self.status='Introduces random mutations into protein sequences.'; return true;" onmouseout="self.status=' '; return true;">-Mutate Protein</a><br />
    <a href="random_coding_dna.html" onmouseover="self.status='Generates a random coding sequence of the length you specify.'; return true;" onmouseout="self.status=' '; return true;">-Random Coding DNA</a><br />
    <a href="random_dna.html" onmouseover="self.status='Generates a random DNA sequence of the length you specify.'; return true;" onmouseout="self.status=' '; return true;">-Random DNA Sequence</a><br />
    <a href="random_dna_regions.html" onmouseover="self.status='Replaces regions of the DNA sequences you enter with random bases.'; return true;" onmouseout="self.status=' '; return true;">-Random DNA Regions</a><br />
    <a href="random_protein.html" onmouseover="self.status='Generates a random protein sequence of the length you specify.'; return true;" onmouseout="self.status=' '; return true;">-Random Protein Sequence</a><br />
    <a href="random_protein_regions.html" onmouseover="self.status='Replaces regions of the protein sequences you enter with random residues.'; return true;" onmouseout="self.status=' '; return true;">-Random Protein Regions</a><br />
    <a href="sample_dna.html" onmouseover="self.status='Samples bases from a DNA sequence with replacement.'; return true;" onmouseout="self.status=' '; return true;">-Sample DNA</a><br />
    <a href="sample_protein.html" onmouseover="self.status='Samples residues from a protein sequence with replacement.'; return true;" onmouseout="self.status=' '; return true;">-Sample Protein</a><br />
    <a href="shuffle_dna.html" onmouseover="self.status='Randomly shuffles the DNA sequences you enter.'; return true;" onmouseout="self.status=' '; return true;">-Shuffle DNA</a><br />
    <a href="shuffle_protein.html" onmouseover="self.status='Randomly shuffles the protein sequences you enter.'; return true;" onmouseout="self.status=' '; return true;">-Shuffle Protein</a>
  </div>

  <div class="category">
    Miscellaneous
  </div>

  <div class="program">
    <a href="iupac.html" onmouseover="self.status='IUPAC codes for DNA and protein.'; return true;" onmouseout="self.status=' '; return true;">-IUPAC codes</a><br />
    <a href="genetic_code.html" onmouseover="self.status='The genetic codes used in the Sequence Manipulation Suite.'; return true;" onmouseout="self.status=' '; return true;">-Genetic codes</a><br />
    <a href="browser_compat.html" onmouseover="self.status='Browser compatibility.'; return true;" onmouseout="self.status=' '; return true;">-Browser compatibility</a><br />
    <a href="mirror.html" onmouseover="self.status='Mirror the Sequence Manipulation Suite.'; return true;" onmouseout="self.status=' '; return true;">-Mirror this site</a><br />
    <a href="mirror.html" onmouseover="self.status='Use the Sequence Manipulation Suite off-line.'; return true;" onmouseout="self.status=' '; return true;">-Use this site off-line</a><br />
    <a href="about.html" onmouseover="self.status='About the Sequence Manipulation Suite.'; return true;" onmouseout="self.status=' '; return true;">-About this site</a><br />
    <a href="acknowledgments.html" onmouseover="self.status='Acknowledgments.'; return true;" onmouseout="self.status=' '; return true;">-Acknowledgments</a><br />
    <a href="reference.html" onmouseover="self.status='Citing the Sequence Manipulation Suite.'; return true;" onmouseout="self.status=' '; return true;">-Reference</a>
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            The Sequence Manipulation Suite Copyright &copy; 2000, 2004 Paul Stothard. Send questions and comments to stothard@ualberta.ca
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                <td class="sms">Sequence Manipulation Suite:</td>
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              <tr>
                <td class="title">GenBank Feature Extractor</td>
              </tr>

              <tr>
                <td class="description">
                  GenBank Feature Extractor accepts a GenBank file as input and reads the sequence feature information described in the feature table, according to the rules outlined in the GenBank release notes. The program extracts or highlights the relevant sequence segments and returns each sequence feature in FASTA format. GenBank Feature Extractor is particularly helpful when you wish to derive the sequence of a cDNA from a genomic sequence that contains many introns.<br />
                  <br />

                  <form action="" name="main_form" id="main_form">
                    Paste the contents of one or more GenBank files into the text area below. Input limit is 200000 characters.<br />
                    <textarea rows="6" cols="81">
LOCUS       AF177870     3123 bp    DNA             INV       31-OCT-1999
DEFINITION  Caenorhabditis remanei putative PP2C protein phosphatase FEM-2
            (fem-2) gene, complete cds.
ACCESSION   AF177870
NID         g6164828
VERSION     AF177870.1  GI:6164828
KEYWORDS    .
SOURCE      Caenorhabditis remanei.
  ORGANISM  Caenorhabditis remanei
            Eukaryota; Metazoa; Nematoda; Secernentea; Rhabditia; Rhabditida;
            Rhabditina; Rhabditoidea; Rhabditidae; Peloderinae; Caenorhabditis.
REFERENCE   1  (bases 1 to 3123)
  AUTHORS   Stothard,P.M., Hansen,D. and Pilgrim,D.
  TITLE     Isolation of PP2C sequences using degenerate-oligo PCR
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3123)
  AUTHORS   Stothard,P.M., Hansen,D. and Pilgrim,D.
  TITLE     Direct Submission
  JOURNAL   Submitted (17-AUG-1999) Biological Sciences, University of Alberta,
            Edmonton, AB T6G-2E9, Canada
FEATURES             Location/Qualifiers
     source          1..3123
                     /organism="Caenorhabditis remanei"
                     /db_xref="taxon:31234"
     mRNA            join(&lt;265..402,673..781,911..1007,1088..1215,
                     1377..1573,1866..2146,2306..2634,2683..&gt;2855)
                     /gene="fem-2"
                     /product="putative FEM-2 protein phosphatase type 2C"
     gene            &lt;265..&gt;2855
                     /gene="fem-2"
     CDS             join(265..402,673..781,911..1007,1088..1215,1377..1573,
                     1866..2146,2306..2634,2683..2855)
                     /gene="fem-2"
                     /note="possible sex-determining protein"
                     /codon_start=1
                     /product="putative PP2C protein phosphatase FEM-2"
                     /protein_id="AAF04557.1"
                     /db_xref="PID:g6164829"
                     /db_xref="GI:6164829"
                     /translation="MSDSLNHPSSSTVHADDGFEPPTSPEDNNKKPSLEQIKQEREAL
                     FTDLFADRRRSARSVIEEAFQNELMSAEPVQPNVPNPHSIPIRFRHQPVAGPAHDVFG
                     DAVHSIFQKIMSRGVNADYSHWMSYWIALGIDKKTQMNYHMKPFCKDTYATEGSLEAK
                     QTFTDKIRSAVEEIIWKSAEYCDILSEKWTGIHVSADQLKGQRNKQEDRFVAYPNGQY
                     MNRGQSDISLLAVFDGHGGHECSQYAAAHFWEAWSDAQHHHSQDMKLDELLEKALETL
                     DERMTVRSVRESWKGGTTAVCCAVDLNTNQIAFAWLGDSPGYIMSNLEFRKFTTEHSP
                     SDPEECRRVEEVGGQIFVIGGELRVNGVLNLTRALGDVPGRPMISNKPDTLLKTIEPA
                     DYLVLLACDGISDVFNTSDLYNLVQAFVNEYDVEDYHELARYICNQAVSAGSADNVTV
                     VIGFLRPPEDVWRVMKTDSDDEESELEEEDDNE"
BASE COUNT      986 a    605 c    597 g    935 t
ORIGIN      
        1 gaacgcgaat gcctctctct ctttcgatgg gtatgccaat tgtccacatt cactcgtgtt
       61 gcctcctctt tgccaacacg caagacacca gaaacgcgtc aaccaaagag aaaaagacgc
      121 cgacaacggg cagcactcgc gagagacaaa ggttatcgcg ttgtgttatt atacattcgc
      181 atccgggtca actttagtcc gttgaacatg cttcttgaaa acctagttct cttaaaataa
      241 cgttttagaa gttttggtct tcagatgtct gattcgctaa atcatccatc gagttctacg
      301 gtgcatgcag atgatggatt cgagccacca acatctccgg aagacaacaa caaaaaaccg
      361 tctttagaac aaattaaaca ggaaagagaa gcgttgttta cggttagtta cctattagct
      421 gcaagttttg aaaaagcgga atctgtaaaa agcggaatct gtaaaaaaaa catctaagga
      481 ataattctga aaagaaaaag tttctaaatg ttaatcggaa tccaattttt atgaaattat
      541 ttaaaaaaaa actaaaatta gtttctaaaa aatttttcta aagtaattgg accatgtgaa
      601 ggtacaccca cttgttccaa tatgccatat ctaactgtaa aataatttga ttctcatgag
      661 aatatttttc aggatctatt cgcagatcgt cgacgaagcg ctcgttctgt gattgaagaa
      721 gctttccaaa acgaactcat gagtgctgaa ccagtccagc caaacgtgcc gaatccacat
      781 tgtgagttgg aaatttttat ttgataacca agagaaaaaa agttctacct ttttttcaaa
      841 aacctttcca aaaatgattc catctgatat aggattaaga aaaatatttt ccgaaatctc
      901 tgcttttcag cgattcccat tcgtttccgt catcaaccag ttgctggacc tgctcatgat
      961 gttttcggag acgcggtgca ttcaattttt caaaaaataa tgtccaggta tacactattt
     1021 ttgcatattt ttcttgccaa atttggtcaa aaaccgtagt acaacccaaa aagtttcttc
     1081 atttcagagg agtgaacgcg gattatagtc attggatgtc atattggatc gcgttgggaa
     1141 tcgacaaaaa aacacaaatg aactatcata tgaaaccgtt ttgcaaagat acttatgcaa
     1201 ctgaaggctc cttaggtagg ttagtctttt ctaggcacag aagagtgaga aaattctaaa
     1261 tttctgagca gtctgctttt tgttttcctt gagtttttac ttaaagctct taaaagaaat
     1321 ctaggcgtga agttcgagcc ttgtaccata ccacaacagc attccaaatg ttacagaagc
     1381 gaaacaaaca tttactgata aaatcaggtc agctgttgag gaaattatct ggaagtccgc
     1441 tgaatattgt gatattctta gcgagaagtg gacaggaatt catgtgtcgg ccgaccaact
     1501 gaaaggtcaa agaaataagc aagaagatcg ttttgtggct tatccaaatg gacaatacat
     1561 gaatcgtgga caggttagtg cgaatcgggg actcaagatt tactgaaata gtgaagagaa
     1621 aacaaaagaa aactatattt tcaaaaaaaa tgagaactct aataaacaga atgaaaaaca
     1681 ttcaaagcta cagtagtatt tccagctgga gtttccagag ccaaaaaaat gcgagtatta
     1741 ctgtagtttt gaaattggtt tctcacttta cgtacgattt tttgattttt ttttcagact
     1801 cttcatatga aaaaaaatca tgttttctcc tttacaagat ttttttgatc tcaaaacatt
     1861 tccagagtga catttcactt cttgcggtgt tcgatgggca tggcggacac gagtgctctc
     1921 aatatgcagc tgctcatttc tgggaagcat ggtccgatgc tcaacatcat cattcacaag
     1981 atatgaaact tgacgaactc ctagaaaagg ctctagaaac attggacgaa agaatgacag
     2041 tcagaagtgt tcgagaatct tggaaaggtg gaaccactgc tgtctgctgt gctgttgatt
     2101 tgaacactaa tcaaatcgca tttgcctggc ttggagattc accagggtaa tcaatttttt
     2161 tttagttttt ggaactttac gtcccgaaaa attattcctt tatcacctaa ttcctacagt
     2221 aacccaagct ccgaattaaa taaagttaaa gcgtggtata cacataaaaa taagaaaaaa
     2281 ttgttcatga aatccatttt tccagttaca tcatgtcaaa cttggagttc cgcaaattca
     2341 ctactgaaca ctccccgtct gacccggagg aatgtcgacg agtcgaagaa gtcggtggcc
     2401 agatttttgt gatcggtggt gagctccgtg tgaatggagt actcaacctg acgcgagcac
     2461 taggagacgt acctggaaga ccaatgatat ccaacaaacc tgatacctta ctgaagacga
     2521 tcgaacctgc ggattatctt gttttgttgg cctgtgacgg gatttctgac gtcttcaaca
     2581 ctagtgattt gtacaatttg gttcaggctt ttgtcaatga atatgacgta gaaggtatca
     2641 aactgatcgt ttttcacatc acaaaattct tgaattttcc agattatcac gaacttgcac
     2701 gctacatttg caatcaagca gtttcagctg gaagtgctga caatgtgaca gtagttatag
     2761 gtttcctccg tccaccagaa gacgtttggc gtgtaatgaa aacagactcg gatgatgaag
     2821 agagcgagct cgaggaagaa gatgacaatg aatagtttat tgcaagtttt ccaaaacttt
     2881 tccaatttcc ctgggtattg attagcatcc atatcttacg gcgattatat caattgtaac
     2941 attatttctg tttctccccc cacctctcaa attttcaaat gacccttttt cttttcgtct
     3001 acctgtatcg ttttccattc atctcccccc ctccactgtg gtatatcatt ttgtcattag
     3061 aaagtattat tttgattttc attggcagta gaagacaaca ggatacagaa gaggttttca
     3121 cag
//
</textarea><br />

                    <div class="warning">
                      Please check the <a href="browser_compat.html">browser compatibility</a> page before using this program.
                    </div><input type="button" value="Submit" name="main_submit" onclick="try{genbankFeat(document)} catch(e) {alert('The following error was encountered: ' + e);}" /> <input type="button" value="Clear" onclick="document.forms[0].elements[0].value = ' '" /> <input type="reset" value="Reset" />

                    <ul>
                      <li>Sequence features should be <select>
                        <option value="separated" selected="selected">
                          separated
                        </option>

                        <option value="uppercased">
                          uppercased
                        </option>
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